
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   17 (  146),  selected   17 , name T0381TS277_3-D1
# Molecule2: number of CA atoms   61 (  477),  selected   17 , name T0381_D1.pdb
# PARAMETERS: T0381TS277_3-D1.T0381_D1.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        62 - 77          4.05     5.13
  LCS_AVERAGE:     25.65

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        65 - 72          1.82     7.62
  LONGEST_CONTINUOUS_SEGMENT:     8        70 - 77          1.98     7.46
  LCS_AVERAGE:     12.15

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        73 - 77          0.96     8.27
  LCS_AVERAGE:      6.65

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:   61
LCS_GDT     V      61     V      61      3    4   10     0    3    3    3    4    5    5    5    5    7    8    8    8    8    8    9   11   12   13   14 
LCS_GDT     E      62     E      62      3    4   16     0    3    4    4    4    6    6    8    9   10   11   13   16   16   16   16   16   16   16   16 
LCS_GDT     L      63     L      63      3    7   16     1    3    4    6    7    9    9   11   12   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     G      64     G      64      3    7   16     1    3    5    6    7    9   10   12   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     Y      65     Y      65      4    8   16     4    5    6    7    9   11   12   13   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     V      66     V      66      4    8   16     3    4    6    7    9   11   12   13   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     A      67     A      67      4    8   16     3    4    5    7    9   11   12   13   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     T      68     T      68      4    8   16     3    4    5    6    9   11   12   13   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     D      69     D      69      4    8   16     3    4    4    6    8    9   12   13   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     G      70     G      70      4    8   16     4    5    6    7    9   11   12   13   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     S      71     S      71      4    8   16     4    5    6    7    9   11   12   13   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     A      72     A      72      4    8   16     4    5    6    7    9   11   12   13   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     F      73     F      73      5    8   16     4    4    5    5    8   10   12   13   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     W      74     W      74      5    8   16     4    4    6    7    9   11   12   13   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     L      75     L      75      5    8   16     4    5    6    7    9   11   12   13   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     T      76     T      76      5    8   16     4    4    6    7    8   11   12   13   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_GDT     P      77     P      77      5    8   16     4    4    5    7    8   11   11   13   13   14   15   15   16   16   16   16   16   16   16   16 
LCS_AVERAGE  LCS_A:  14.82  (   6.65   12.15   25.65 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA      4      5      6      7      9     11     12     13     13     14     15     15     16     16     16     16     16     16     16     16 
GDT PERCENT_CA   6.56   8.20   9.84  11.48  14.75  18.03  19.67  21.31  21.31  22.95  24.59  24.59  26.23  26.23  26.23  26.23  26.23  26.23  26.23  26.23
GDT RMS_LOCAL    0.11   0.64   0.95   1.23   1.52   2.06   2.36   2.52   2.52   2.80   3.38   3.38   4.05   4.05   4.05   4.05   4.05   4.05   4.05   4.05
GDT RMS_ALL_CA   7.56   6.51   6.17   6.16   7.29   6.59   6.99   6.88   6.88   6.31   5.51   5.51   5.13   5.13   5.13   5.13   5.13   5.13   5.13   5.13

#      Molecule1      Molecule2       DISTANCE
LGA    V      61      V      61         18.547
LGA    E      62      E      62         16.144
LGA    L      63      L      63         12.393
LGA    G      64      G      64          6.441
LGA    Y      65      Y      65          2.938
LGA    V      66      V      66          2.570
LGA    A      67      A      67          2.701
LGA    T      68      T      68          2.944
LGA    D      69      D      69          3.754
LGA    G      70      G      70          1.439
LGA    S      71      S      71          1.508
LGA    A      72      A      72          1.432
LGA    F      73      F      73          3.696
LGA    W      74      W      74          2.149
LGA    L      75      L      75          0.824
LGA    T      76      T      76          2.573
LGA    P      77      P      77          2.808

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17   61    4.0     13    2.52    16.803    16.634     0.496

LGA_LOCAL      RMSD =  2.519  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.215  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  5.024  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.437092 * X  +  -0.706066 * Y  +  -0.557154 * Z  +  36.002644
  Y_new =  -0.316241 * X  +  -0.459261 * Y  +   0.830103 * Z  +  79.290329
  Z_new =  -0.841987 * X  +   0.539027 * Y  +  -0.022547 * Z  +  37.226868 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.612602   -1.528991  [ DEG:    92.3953    -87.6047 ]
  Theta =   1.000956    2.140637  [ DEG:    57.3505    122.6495 ]
  Phi   =  -2.515262    0.626331  [ DEG:  -144.1139     35.8861 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0381TS277_3-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS277_3-D1.T0381_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17   61   4.0   13   2.52  16.634     5.02
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS277_3-D1
PFRMAT TS 
TARGET T0381
MODEL 3
PARENT 1TF1_A
ATOM      1  H   VAL    61      29.908  46.821  11.181  1.00  0.00                              
ATOM      3  N   VAL    61      29.488  46.349  11.875  1.00  0.00                              
ATOM      5  CA  VAL    61      28.283  46.908  12.481  1.00  0.00                              
ATOM      7  CB  VAL    61      27.864  46.102  13.730  1.00  0.00                              
ATOM      9  C   VAL    61      28.541  48.355  12.884  1.00  0.00                              
ATOM     11  O   VAL    61      29.496  48.637  13.611  1.00  0.00                              
ATOM     13  CG1 VAL    61      27.929  44.605  13.449  1.00  0.00                              
ATOM     15  CG2 VAL    61      28.753  46.466  14.913  1.00  0.00                              
ATOM     17  H   GLU    62      27.046  49.034  11.780  1.00  0.00                              
ATOM     19  N   GLU    62      27.729  49.283  12.384  1.00  0.00                              
ATOM     21  CA  GLU    62      27.876  50.686  12.764  1.00  0.00                              
ATOM     23  CB  GLU    62      29.342  51.130  12.652  1.00  0.00                              
ATOM     25  C   GLU    62      26.979  51.614  11.948  1.00  0.00                              
ATOM     27  O   GLU    62      27.353  52.020  10.845  1.00  0.00                              
ATOM     29  CG  GLU    62      29.885  51.223  11.228  1.00  0.00                              
ATOM     31  CD  GLU    62      31.325  51.718  11.151  1.00  0.00                              
ATOM     33  OE1 GLU    62      31.763  52.429  12.084  1.00  0.00                              
ATOM     35  OE2 GLU    62      32.021  51.426  10.146  1.00  0.00                              
ATOM     37  H   LEU    63      25.542  51.641  13.315  1.00  0.00                              
ATOM     39  N   LEU    63      25.819  51.988  12.480  1.00  0.00                              
ATOM     41  CA  LEU    63      24.973  52.942  11.773  1.00  0.00                              
ATOM     43  CB  LEU    63      25.023  52.682  10.270  1.00  0.00                              
ATOM     45  C   LEU    63      23.520  52.928  12.239  1.00  0.00                              
ATOM     47  O   LEU    63      22.608  52.973  11.410  1.00  0.00                              
ATOM     49  CG  LEU    63      24.020  53.495   9.459  1.00  0.00                              
ATOM     51  CD1 LEU    63      24.321  54.981   9.604  1.00  0.00                              
ATOM     53  CD2 LEU    63      24.057  53.078   7.996  1.00  0.00                              
ATOM     55  H   GLY    64      23.995  52.868  14.151  1.00  0.00                              
ATOM     57  N   GLY    64      23.285  52.908  13.549  1.00  0.00                              
ATOM     59  CA  GLY    64      21.918  52.885  14.043  1.00  0.00                              
ATOM     61  C   GLY    64      21.629  53.781  15.232  1.00  0.00                              
ATOM     63  O   GLY    64      22.169  53.586  16.322  1.00  0.00                              
ATOM     65  H   TYR    65      20.192  54.718  14.265  1.00  0.00                              
ATOM     67  N   TYR    65      20.709  54.718  15.055  1.00  0.00                              
ATOM     69  CA  TYR    65      20.422  55.703  16.083  1.00  0.00                              
ATOM     71  CB  TYR    65      21.733  56.264  16.653  1.00  0.00                              
ATOM     73  C   TYR    65      19.577  56.825  15.484  1.00  0.00                              
ATOM     75  O   TYR    65      19.296  56.808  14.284  1.00  0.00                              
ATOM     77  CG  TYR    65      22.488  57.212  15.740  1.00  0.00                              
ATOM     79  CD1 TYR    65      22.296  57.213  14.357  1.00  0.00                              
ATOM     81  CE1 TYR    65      22.998  58.092  13.534  1.00  0.00                              
ATOM     83  CZ  TYR    65      23.897  58.982  14.097  1.00  0.00                              
ATOM     85  CD2 TYR    65      23.379  58.136  16.282  1.00  0.00                              
ATOM     87  CE2 TYR    65      24.086  59.017  15.468  1.00  0.00                              
ATOM     89  OH  TYR    65      24.576  59.870  13.291  1.00  0.00                              
ATOM     91  H   VAL    66      19.445  57.798  17.192  1.00  0.00                              
ATOM     93  N   VAL    66      19.160  57.791  16.299  1.00  0.00                              
ATOM     95  CA  VAL    66      18.296  58.867  15.817  1.00  0.00                              
ATOM     97  CB  VAL    66      17.743  59.720  16.981  1.00  0.00                              
ATOM     99  C   VAL    66      19.052  59.770  14.844  1.00  0.00                              
ATOM    101  O   VAL    66      20.178  60.191  15.118  1.00  0.00                              
ATOM    103  CG1 VAL    66      16.797  58.903  17.854  1.00  0.00                              
ATOM    105  CG2 VAL    66      18.890  60.275  17.820  1.00  0.00                              
ATOM    107  H   ALA    67      17.605  59.657  13.525  1.00  0.00                              
ATOM    109  N   ALA    67      18.436  60.045  13.696  1.00  0.00                              
ATOM    111  CA  ALA    67      19.005  60.950  12.707  1.00  0.00                              
ATOM    113  CB  ALA    67      19.521  60.171  11.500  1.00  0.00                              
ATOM    115  C   ALA    67      17.938  61.951  12.273  1.00  0.00                              
ATOM    117  O   ALA    67      16.967  62.166  13.003  1.00  0.00                              
ATOM    119  H   THR    68      18.845  62.279  10.560  1.00  0.00                              
ATOM    121  N   THR    68      18.111  62.530  11.086  1.00  0.00                              
ATOM    123  CA  THR    68      17.212  63.561  10.567  1.00  0.00                              
ATOM    125  CB  THR    68      17.638  63.964   9.134  1.00  0.00                              
ATOM    127  C   THR    68      15.762  63.079  10.556  1.00  0.00                              
ATOM    129  O   THR    68      15.446  62.071   9.921  1.00  0.00                              
ATOM    131  CG2 THR    68      16.801  65.111   8.572  1.00  0.00                              
ATOM    133  OG1 THR    68      19.015  64.362   9.153  1.00  0.00                              
ATOM    135  H   ASP    69      15.166  64.588  11.680  1.00  0.00                              
ATOM    137  N   ASP    69      14.876  63.815  11.226  1.00  0.00                              
ATOM    139  CA  ASP    69      13.458  63.459  11.273  1.00  0.00                              
ATOM    141  CB  ASP    69      13.024  63.153  12.710  1.00  0.00                              
ATOM    143  C   ASP    69      12.580  64.570  10.706  1.00  0.00                              
ATOM    145  O   ASP    69      12.142  65.459  11.441  1.00  0.00                              
ATOM    147  CG  ASP    69      11.560  62.769  12.815  1.00  0.00                              
ATOM    149  OD1 ASP    69      10.855  62.800  11.783  1.00  0.00                              
ATOM    151  OD2 ASP    69      11.111  62.415  13.927  1.00  0.00                              
ATOM    153  H   GLY    70      12.580  63.785   8.904  1.00  0.00                              
ATOM    155  N   GLY    70      12.278  64.505   9.413  1.00  0.00                              
ATOM    157  CA  GLY    70      11.468  65.533   8.781  1.00  0.00                              
ATOM    159  C   GLY    70       9.999  65.160   8.689  1.00  0.00                              
ATOM    161  O   GLY    70       9.165  65.990   8.319  1.00  0.00                              
ATOM    163  H   SER    71      10.337  63.338   9.342  1.00  0.00                              
ATOM    165  N   SER    71       9.673  63.921   9.040  1.00  0.00                              
ATOM    167  CA  SER    71       8.298  63.438   8.956  1.00  0.00                              
ATOM    169  CB  SER    71       7.739  63.674   7.550  1.00  0.00                              
ATOM    171  C   SER    71       8.216  61.955   9.299  1.00  0.00                              
ATOM    173  O   SER    71       7.206  61.303   9.024  1.00  0.00                              
ATOM    175  OG  SER    71       8.685  63.293   6.565  1.00  0.00                              
ATOM    177  H   ALA    72      10.009  61.966  10.101  1.00  0.00                              
ATOM    179  N   ALA    72       9.284  61.419   9.882  1.00  0.00                              
ATOM    181  CA  ALA    72       9.342  59.998  10.211  1.00  0.00                              
ATOM    183  CB  ALA    72       7.934  59.435  10.376  1.00  0.00                              
ATOM    185  C   ALA    72      10.094  59.223   9.133  1.00  0.00                              
ATOM    187  O   ALA    72       9.961  59.516   7.943  1.00  0.00                              
ATOM    189  H   PHE    73      10.966  58.062  10.474  1.00  0.00                              
ATOM    191  N   PHE    73      10.900  58.252   9.549  1.00  0.00                              
ATOM    193  CA  PHE    73      11.694  57.469   8.609  1.00  0.00                              
ATOM    195  CB  PHE    73      12.007  58.303   7.359  1.00  0.00                              
ATOM    197  C   PHE    73      12.991  56.998   9.258  1.00  0.00                              
ATOM    199  O   PHE    73      13.777  56.278   8.639  1.00  0.00                              
ATOM    201  CG  PHE    73      12.912  57.611   6.373  1.00  0.00                              
ATOM    203  CD1 PHE    73      12.441  56.554   5.602  1.00  0.00                              
ATOM    205  CE1 PHE    73      13.272  55.918   4.683  1.00  0.00                              
ATOM    207  CZ  PHE    73      14.591  56.328   4.544  1.00  0.00                              
ATOM    209  CD2 PHE    73      14.223  58.039   6.197  1.00  0.00                              
ATOM    211  CE2 PHE    73      15.065  57.399   5.291  1.00  0.00                              
ATOM    213  H   TRP    74      12.573  57.950  10.941  1.00  0.00                              
ATOM    215  N   TRP    74      13.201  57.381  10.514  1.00  0.00                              
ATOM    217  CA  TRP    74      14.395  56.967  11.243  1.00  0.00                              
ATOM    219  CB  TRP    74      14.920  58.117  12.115  1.00  0.00                              
ATOM    221  C   TRP    74      14.118  55.734  12.096  1.00  0.00                              
ATOM    223  O   TRP    74      12.971  55.293  12.206  1.00  0.00                              
ATOM    225  CG  TRP    74      13.899  58.707  13.036  1.00  0.00                              
ATOM    227  CD1 TRP    74      13.123  59.811  12.827  1.00  0.00                              
ATOM    229  NE1 TRP    74      12.315  60.027  13.917  1.00  0.00                              
ATOM    231  HE1 TRP    74      11.673  60.725  13.992  1.00  0.00                              
ATOM    233  CD2 TRP    74      13.510  58.172  14.302  1.00  0.00                              
ATOM    235  CE2 TRP    74      12.555  59.054  14.849  1.00  0.00                              
ATOM    237  CE3 TRP    74      13.954  57.091  15.073  1.00  0.00                              
ATOM    239  CZ3 TRP    74      13.479  56.957  16.369  1.00  0.00                              
ATOM    241  CH2 TRP    74      12.566  57.877  16.902  1.00  0.00                              
ATOM    243  CZ2 TRP    74      12.092  58.930  16.160  1.00  0.00                              
ATOM    245  H   LEU    75      16.039  55.462  12.456  1.00  0.00                              
ATOM    247  N   LEU    75      15.170  55.147  12.654  1.00  0.00                              
ATOM    249  CA  LEU    75      15.023  53.997  13.537  1.00  0.00                              
ATOM    251  CB  LEU    75      13.550  53.757  13.878  1.00  0.00                              
ATOM    253  C   LEU    75      15.623  52.743  12.907  1.00  0.00                              
ATOM    255  O   LEU    75      15.137  52.266  11.879  1.00  0.00                              
ATOM    257  CG  LEU    75      13.268  52.616  14.858  1.00  0.00                              
ATOM    259  CD1 LEU    75      13.936  52.905  16.195  1.00  0.00                              
ATOM    261  CD2 LEU    75      11.767  52.435  15.038  1.00  0.00                              
ATOM    263  H   THR    76      17.042  52.643  14.265  1.00  0.00                              
ATOM    265  N   THR    76      16.691  52.224  13.505  1.00  0.00                              
ATOM    267  CA  THR    76      17.365  51.036  12.986  1.00  0.00                              
ATOM    269  CB  THR    76      18.120  51.354  11.677  1.00  0.00                              
ATOM    271  C   THR    76      18.356  50.486  14.012  1.00  0.00                              
ATOM    273  O   THR    76      19.433  51.054  14.205  1.00  0.00                              
ATOM    275  CG2 THR    76      18.411  50.080  10.892  1.00  0.00                              
ATOM    277  OG1 THR    76      17.323  52.226  10.867  1.00  0.00                              
ATOM    279  N   PRO    77      17.997  49.410  14.719  1.00  0.00                              
ATOM    281  CA  PRO    77      18.875  48.810  15.724  1.00  0.00                              
ATOM    283  CB  PRO    77      17.842  48.425  16.776  1.00  0.00                              
ATOM    285  C   PRO    77      19.577  47.550  15.228  1.00  0.00                              
ATOM    287  O   PRO    77      19.642  46.553  15.958  1.00  0.00                              
ATOM    289  CG  PRO    77      16.721  47.868  15.945  1.00  0.00                              
ATOM    291  CD  PRO    77      16.702  48.706  14.681  1.00  0.00                              
TER 
END
